title: SmoWT-MB, DMSO, i.g., rep1

description:
subWT_D_1
InVivo_P60+P7+WT_Cerebellum+GDC_Count+FPKM.txt


title: SmoWT-MB, GDC-0449, 24h, ex vivo, rep2

status: Public on May 16 2024

type: SRA

city: Shanghai

first: Yi

last: Sui

address: South Chongqing Road

country: China

institute: Shanghai Jiao Tong University School of Medicine

description:
SmoWT_GDC01uM_24hr_6
ExVivo_56+WT_GDC_Count+FPKM.txt

library_source: transcriptomic

data_processing:
Trim galore was used to automatically detect and trim adapters.
Reads were mapped to GRCh38 or GRCm38 reference genome using Hisat2.
Counts were generated using HTSeq (version 0.11.1).
Assembly: hg38 for Homo sapiens samples, mm10 for Mus musculus samples.
Supplementary files format and content: txt files included raw counts and FPKM for each Sample

molecule: total RNA

organism: Mus musculus

source_name: SmoWT-MB cells freshly constructed from subcutaneous allograft

extract_protocol:
Cells treated with corresponding small molecular inhibitors and mouse cerebellum tissues were harvested and lysed in Trizol. Samples for RNA-seq assays were then sent to MAJORBIO company (Shanghai, China) for RNA extraction.
Samples for RNA-seq assays were sent to MAJORBIO company (Shanghai, China) for library construction and second-generation sequencing.

tag: cell line

tag: cell type

value: mouse SHH-subtype medulloblastoma cells

tag: genotype

tag: treatment

value: 0.1μM GDC-0449 treated for 24h


title: peripheral-blood-dna_cancer-patient-152

type: genomic

city: Singapore

first: Ann

last: Lee

address: 30 Hospital Boulevard

department: Division of Cellular and Molecular Research

country: Singapore

institute: National Cancer Centre Singapore

description:
cancer patient peripheral blood
A0394

hyb_protocol: Bisulfite-converted DNA was amplified and hybridised onto Illumina MethylationEPIC beadchip using standard Illumina protocol

scan_protocol: Arrays were scanned using the Illumina iScan scanner using standard Illumina protocol

data_processing:
Using R/Bioconductor minfi: Probes located near known SNPs of any frequency, or probes known to be cross-reactive were removed. Then, each sample was normalized independently via intra-sample BMIQ normalization.
BMIQ-normalized beta values, after removing probes near SNPs and cross-reactive probes
Unmethylated and methylated signal intensities

label: Cy5, Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood DNA, cancer patient 152

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from whole blood or buffy coat using the Qiagen QIAamp DNA Blood Kit according to standard instructions

tag: condition

value: affected


title: peripheral-blood-dna_cancer-patient-153

description:
cancer patient peripheral blood
A0942

source_name: Peripheral blood DNA, cancer patient 153


title: peripheral-blood-dna_cancer-patient-151

description:
cancer patient peripheral blood
A0962

source_name: Peripheral blood DNA, cancer patient 151


title: SmoWT-MB, GDC-0449, 24h, ex vivo, rep1

description:
SmoWT_GDC01uM_24hr_5
ExVivo_56+WT_GDC_Count+FPKM.txt

value: SmoWT-MB cells freshly constructed from subcutaneous allograft


title: peripheral-blood-dna_cancer-patient-154

description:
cancer patient peripheral blood
A0453

source_name: Peripheral blood DNA, cancer patient 154


title: SmoWT-MB, DMSO, 24h, ex vivo, rep1

description:
SmoWT_DMSO_24hr_1
ExVivo_56+WT_GDC_Count+FPKM.txt

value: 0.1% DMSO treated for 24h


title: SmoWT-MB, DMSO, 24h, ex vivo, rep2

description:
SmoWT_DMSO_24hr_2
ExVivo_56+WT_GDC_Count+FPKM.txt


title: peripheral-blood-dna_cancer-patient-162

description:
cancer patient peripheral blood
A0853

source_name: Peripheral blood DNA, cancer patient 162


title: peripheral-blood-dna_cancer-patient-148

description:
cancer patient peripheral blood
A0877

source_name: Peripheral blood DNA, cancer patient 148


title: peripheral-blood-dna_cancer-patient-147

description:
cancer patient peripheral blood
A0842

source_name: Peripheral blood DNA, cancer patient 147


title: SmoWT-MB, GDC-0449, 24h, in vitro, rep1

description:
L1EGG192443--WT_G01_1
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt

source_name: SmoWT-MB

value: SmoWT-MB


title: peripheral-blood-dna_cancer-patient-150

description:
cancer patient peripheral blood
A0792

source_name: Peripheral blood DNA, cancer patient 150


title: SmoWT-MB, DMSO, 24h, in vitro, rep2

description:
L1EGG192442--WT_DMSO_2
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt


title: peripheral-blood-dna_cancer-patient-156

description:
cancer patient peripheral blood
A0827

source_name: Peripheral blood DNA, cancer patient 156


title: SmoWT-MB, DMSO, 24h, in vitro, rep1

description:
L1EGG192441--WT_DMSO_1
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt


title: SmoWT-MB, GDC-0449, 24h, in vitro, rep2

description:
L1EGG192444--WT_G01_2
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt


title: peripheral-blood-dna_cancer-patient-146

description:
cancer patient peripheral blood
A0953

source_name: Peripheral blood DNA, cancer patient 146


title: peripheral-blood-dna_cancer-patient-149

description:
cancer patient peripheral blood
A0772

source_name: Peripheral blood DNA, cancer patient 149


title: SmoWT-MB, THZ1, 8h, in vitro, rep1

description:
R2-1
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt

value: 0.1μM THZ1 treated for 8h


title: SmoWT-MB, THZ1, 8h, in vitro, rep2

description:
R2-2
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt


title: peripheral-blood-dna_cancer-patient-145

description:
cancer patient peripheral blood
A1077

source_name: Peripheral blood DNA, cancer patient 145


title: peripheral-blood-dna_cancer-patient-144

description:
cancer patient peripheral blood
A0949

source_name: Peripheral blood DNA, cancer patient 144


title: peripheral-blood-dna_cancer-patient-143

description:
cancer patient peripheral blood
A0995

source_name: Peripheral blood DNA, cancer patient 143


title: SmoWT-MB, JQ1, 8h, in vitro, rep1

description:
R3-1
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt

value: 1μM JQ1 treated for 8h


title: peripheral-blood-dna_cancer-patient-142

description:
cancer patient peripheral blood
A0838

source_name: Peripheral blood DNA, cancer patient 142


title: peripheral-blood-dna_cancer-patient-141

description:
cancer patient peripheral blood
BL1206

source_name: Peripheral blood DNA, cancer patient 141


title: SmoWT-MB-GLI2-deltaN, Input

library_source: genomic

data_processing:
ChIP-seq reads were aligned to GRCh38 or GRCm38 reference genome using Bowtie 2 (version 2.3.0).
BAM files were converted by SAMtools (version 1.9).
H3K27ac peaks were called by MACS2 (version 2.2.6) with a q-value threshold of 0.05.
Active enhancers were called by ROSE2 with a stitching distance of 12.5 kb and a transcription start site (TSS) exclusion distance of 2.5 kb.
Super-enhancers were ranked and identified by the Rank Ordering of Super-Enhancers (ROSE) algorithm, and annotated to the closest gene with a certain level of mRNA expression (FPKM > 1).
Assembly: hg38 for Homo sapiens samples, mm10 for Mus musculus samples.
Supplementary files format and content: bigWig

source_name: SmoWT-MB cells stably expressing an active form of HA-tagged human GLI2 without the N-terminal region

extract_protocol:
Cell samples were incubated with 1% formaldehyde to crosslink the protein-DNA complexes and subsequently quenched the formaldehyde by adding 125 mM glycine. Samples for ChIP-seq assays were then frozen in liquid nitrogen, and sent to ROMICS company (Shanghai, China) for sonication, chromatin immunoprecipitation, and DNA extraction.
Samples for ChIP-seq assays were sent to ROMICS company (Shanghai, China) for library construction and second-generation sequencing.

tag: chip antibody


title: peripheral-blood-dna_cancer-patient-140

description:
cancer patient peripheral blood
BS287

source_name: Peripheral blood DNA, cancer patient 140


title: peripheral-blood-dna_cancer-patient-137

description:
cancer patient peripheral blood
BL1451

source_name: Peripheral blood DNA, cancer patient 137


title: peripheral-blood-dna_cancer-patient-139

description:
cancer patient peripheral blood
BL391

source_name: Peripheral blood DNA, cancer patient 139


title: SMB56-2, Input

source_name: SMB56 cells freshly constructed from subcutaneous allograft


title: SmoWT-MB, DMSO, 8h, in vitro, rep1

description:
R1-1
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt

value: 0.1% DMSO treated for 8h


title: SMB56-1, Input


title: peripheral-blood-dna_cancer-patient-136

description:
cancer patient peripheral blood
BS337

source_name: Peripheral blood DNA, cancer patient 136


title: peripheral-blood-dna_cancer-patient-135

description:
cancer patient peripheral blood
SG1305

source_name: Peripheral blood DNA, cancer patient 135


title: peripheral-blood-dna_cancer-patient-134

description:
cancer patient peripheral blood
BL465

source_name: Peripheral blood DNA, cancer patient 134


title: peripheral-blood-dna_cancer-patient-132

description:
cancer patient peripheral blood
SG1449

source_name: Peripheral blood DNA, cancer patient 132


title: SmoWT-2, H3K27ac, ChIP

source_name: SmoWT-MB cells freshly constructed from subcutaneous allograft

value: H3K27ac (Active Motif, #39133)


title: SmoWT-1, Input

source_name: SmoWT-MB


title: peripheral-blood-dna_cancer-patient-138

description:
cancer patient peripheral blood
SG1271

source_name: Peripheral blood DNA, cancer patient 138


title: SmoWT-MB, JQ1, 8h, in vitro, rep2

description:
R3-2
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt


title: peripheral-blood-dna_cancer-patient-133

description:
cancer patient peripheral blood
BS801

source_name: Peripheral blood DNA, cancer patient 133


title: SMB56-1, H3K27ac, ChIP


title: peripheral-blood-dna_cancer-patient-130

description:
cancer patient peripheral blood
BL1714

source_name: Peripheral blood DNA, cancer patient 130


title: peripheral-blood-dna_cancer-patient-131

description:
cancer patient peripheral blood
BL1326

source_name: Peripheral blood DNA, cancer patient 131


title: SmoWT-1, H3K27ac, ChIP


title: peripheral-blood-dna_cancer-patient-129

description:
cancer patient peripheral blood
BS571

source_name: Peripheral blood DNA, cancer patient 129


title: SmoWT-MB, DMSO, 8h, in vitro, rep2

description:
R1-2
InVitro_56+WT_JQ1+THZ1+GDC_Count+FPKM.txt


title: B3(Group B)

city: Tianjin

first: Ting

last: Zheng

state: Tianjin

address: No.154 Anshan Road, Heping District, Tianjin, China

institute: Tianjin Medical University General Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. In this step, clean data (clean reads) were obtained.
Q20, Q30, GC-content and sequence duplication level of the clean data were calculated.
Paired-end clean reads were aligned to the reference genome- GRCm38 using TopHat2/Bowtie2.
Mapped reads were used for the Quantification of gene expression level and Differential expression analysis.
Assembly: GRCm38
Supplementary files format and content: All_miRNA.count
Supplementary files format and content: All_miRNA.count

source_name: adipose

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle medium (DMEM)/F12 supplemented with 10% fetal bovine serum, and 100 U/ml penicillin-streptomycin. All cells were cultured at 37℃ with 5% CO2.

extract_protocol:
Exosomes was isolated from the supernatants of MSC and LPS-treated MSC by untracentrifugation.The total RNA from exosomes was extracted using miRNeasy Serum/Plasma Advanced Kit (Qiagen, cat. No. 217204).
For small RNA libraries, a total amount of 3ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using QIAseq miRNA Library Kit (Qiagen, Frederick, MD) and index codes were added to attribute sequences to each sample.

treatment_protocol: MSC at the 3th-5th passages were used for the subsequent experiments. For LPS preconditioning, MSCs, confluence of 70-80%, were cultured in serum-free medium with LPS (1μm/ml) or PBS for 48h prior to supernatant collection.

tag: tissue

value: adipose

value: primary cell

value: Mesenchymal Stem Cells

value: WT

value: LPS


title: SmoWT-MB-GLI2-deltaN, HA-tag, ChIP

source_name: SmoWT-MB cells stably expressing an active form of HA-tagged human GLI2 without the N-terminal region

value: HA-Tag (Cell Signaling Technology, #3724S)


title: B1(Group B)


title: peripheral-blood-dna_cancer-patient-127

description:
cancer patient peripheral blood
BL1687

source_name: Peripheral blood DNA, cancer patient 127


title: SMB56-2, H3K27ac, ChIP

value: SMB56 cells freshly constructed from subcutaneous allograft


title: A3(Group A)

value: PBS


title: peripheral-blood-dna_cancer-patient-126

description:
cancer patient peripheral blood
BL1640

source_name: Peripheral blood DNA, cancer patient 126


title: peripheral-blood-dna_cancer-patient-125

description:
cancer patient peripheral blood
BL1341

source_name: Peripheral blood DNA, cancer patient 125


title: SmoWT-2, Input

value: mouse SHH-subtype medulloblastoma cells


title: A1(Group A)


title: peripheral-blood-dna_cancer-patient-124

description:
cancer patient peripheral blood
BL381

source_name: Peripheral blood DNA, cancer patient 124

value: affected


title: peripheral-blood-dna_cancer-patient-123

description:
cancer patient peripheral blood
BL2208

source_name: Peripheral blood DNA, cancer patient 123


title: peripheral-blood-dna_cancer-patient-122

description:
cancer patient peripheral blood
SG1192

source_name: Peripheral blood DNA, cancer patient 122


title: 73412DCN

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

country: USA

institute: University of Minnesota

data_processing:
Raw, paired reads were processed via CHURP pipeline (https://github.com/msi-ris/CHURP) using default setting.
The cleaned gene count table per sample was analyzed with R (v4.1.0) package edgeR to identify differentially expressed genes.
R package clusterProfiler was used for pathway enrichment. R package GSVA was used for pathway activity score calculate. Various R packages, including pheatmap and ggplto2, were used to generate visualization plots.
Assembly: GRCm38
Supplementary files format and content: Txt file of tab-separated values.

source_name: Deep Cerebellar Nuclei

extract_protocol:
RNA was extracted using TRIZOL extraction protocol, 3nl of total RNA used for construction of libraries.
Library construction and sequencing were done by University of Minnesota Genomic Center according to the manufacturer’s instructions (Illumina TruSeq Stranded).

value: Deep Cerebellar Nuclei


title: peripheral-blood-dna_cancer-patient-121

description:
cancer patient peripheral blood
MR0077

source_name: Peripheral blood DNA, cancer patient 121


title: 73412CCPV

source_name: Cerebellar Cortex Posterior Vermis

value: Cerebellar Cortex Posterior Vermis


title: peripheral-blood-dna_cancer-patient-120

description:
cancer patient peripheral blood
HR0044

source_name: Peripheral blood DNA, cancer patient 120


title: 73412CCH

source_name: Cerebellar Cortex Hemisphere

value: Cerebellar Cortex Hemisphere


title: 73412CCAV

source_name: Cerebellar Cortex Anterior Vermis

value: Cerebellar Cortex Anterior Vermis


title: peripheral-blood-dna_cancer-patient-119

description:
cancer patient peripheral blood
HR0047

source_name: Peripheral blood DNA, cancer patient 119


title: 73184CCPV


title: B2(Group B)


title: peripheral-blood-dna_cancer-patient-128

description:
cancer patient peripheral blood
BL2473

source_name: Peripheral blood DNA, cancer patient 128


title: peripheral-blood-dna_cancer-patient-116

description:
cancer patient peripheral blood
X66

source_name: Peripheral blood DNA, cancer patient 116


title: peripheral-blood-dna_cancer-patient-117

description:
cancer patient peripheral blood
X126

source_name: Peripheral blood DNA, cancer patient 117


title: 73184CCH


title: peripheral-blood-dna_cancer-patient-118

description:
cancer patient peripheral blood
LR0043

source_name: Peripheral blood DNA, cancer patient 118


title: peripheral-blood-dna_cancer-patient-114

description:
cancer patient peripheral blood
X202

source_name: Peripheral blood DNA, cancer patient 114


title: peripheral-blood-dna_cancer-patient-115

description:
cancer patient peripheral blood
X241

source_name: Peripheral blood DNA, cancer patient 115


title: 72683CCH


title: 73184CCAV


title: 72683CCAV


title: A2(Group A)

source_name: adipose


title: 72683DCN


title: 72683CCPV


title: peripheral-blood-dna_cancer-patient-110

description:
cancer patient peripheral blood
X101

source_name: Peripheral blood DNA, cancer patient 110


title: peripheral-blood-dna_cancer-patient-111

description:
cancer patient peripheral blood
X113

source_name: Peripheral blood DNA, cancer patient 111


title: 73413DCN


title: 72680DCN


title: 72680CCH


title: peripheral-blood-dna_cancer-patient-108

description:
cancer patient peripheral blood
X73

source_name: Peripheral blood DNA, cancer patient 108


title: 72680CCPV


title: peripheral-blood-dna_cancer-patient-107

description:
cancer patient peripheral blood
X156

source_name: Peripheral blood DNA, cancer patient 107


title: 72680CCAV


title: 72195DCN

source_name: Deep Cerebellar Nuclei


title: 72192DCN


title: peripheral-blood-dna_cancer-patient-106

description:
cancer patient peripheral blood
X115

source_name: Peripheral blood DNA, cancer patient 106


title: peripheral-blood-dna_cancer-patient-113

description:
cancer patient peripheral blood
X192

source_name: Peripheral blood DNA, cancer patient 113


title: 72192CCPV

source_name: Cerebellar Cortex Posterior Vermis


title: peripheral-blood-dna_cancer-patient-104

description:
cancer patient peripheral blood
X118

source_name: Peripheral blood DNA, cancer patient 104


title: peripheral-blood-dna_cancer-patient-105

description:
cancer patient peripheral blood
X92

source_name: Peripheral blood DNA, cancer patient 105


title: 72192CCH

source_name: Cerebellar Cortex Hemisphere


title: 72192CCAV

source_name: Cerebellar Cortex Anterior Vermis


title: peripheral-blood-dna_cancer-patient-103

description:
cancer patient peripheral blood
X240

source_name: Peripheral blood DNA, cancer patient 103


title: peripheral-blood-dna_cancer-patient-112

description:
cancer patient peripheral blood
X201

source_name: Peripheral blood DNA, cancer patient 112


title: 72191DCN


title: peripheral-blood-dna_cancer-patient-101

description:
cancer patient peripheral blood
X169

source_name: Peripheral blood DNA, cancer patient 101


title: peripheral-blood-dna_cancer-patient-102

description:
cancer patient peripheral blood
X213

source_name: Peripheral blood DNA, cancer patient 102


title: 72191CCPV


title: 72191CCAV


title: peripheral-blood-dna_cancer-patient-99

description:
cancer patient peripheral blood
X127

source_name: Peripheral blood DNA, cancer patient 99


title: peripheral-blood-dna_cancer-patient-100

description:
cancer patient peripheral blood
X94

source_name: Peripheral blood DNA, cancer patient 100


title: 72191CCH


title: 72095DCN


title: peripheral-blood-dna_cancer-patient-98

description:
cancer patient peripheral blood
X117

source_name: Peripheral blood DNA, cancer patient 98


title: 72095CCH


title: peripheral-blood-dna_cancer-patient-94

description:
cancer patient peripheral blood
YP9

source_name: Peripheral blood DNA, cancer patient 94


title: peripheral-blood-dna_cancer-patient-97

description:
cancer patient peripheral blood
FH92

source_name: Peripheral blood DNA, cancer patient 97


title: 72094DCN

source_name: Deep Cerebellar Nuclei


title: peripheral-blood-dna_cancer-patient-109

description:
cancer patient peripheral blood
X174

source_name: Peripheral blood DNA, cancer patient 109


title: 72095CCPV


title: peripheral-blood-dna_cancer-patient-93

description:
cancer patient peripheral blood
YP38

source_name: Peripheral blood DNA, cancer patient 93


title: 72095CCAV


title: 72094CCH


title: 72094CCPV

source_name: Cerebellar Cortex Posterior Vermis


title: peripheral-blood-dna_cancer-patient-96

description:
cancer patient peripheral blood
FH85

source_name: Peripheral blood DNA, cancer patient 96


title: peripheral-blood-dna_cancer-patient-92

description:
cancer patient peripheral blood
YP23

source_name: Peripheral blood DNA, cancer patient 92


title: 72094CCAV


title: peripheral-blood-dna_cancer-patient-91

description:
cancer patient peripheral blood
YP17

source_name: Peripheral blood DNA, cancer patient 91


title: 71991DCN


title: peripheral-blood-dna_cancer-patient-90

description:
cancer patient peripheral blood
YP20

source_name: Peripheral blood DNA, cancer patient 90


title: 71991CCPV


title: 71991CCH

source_name: Cerebellar Cortex Hemisphere


title: peripheral-blood-dna_cancer-patient-88

description:
cancer patient peripheral blood
YP56

source_name: Peripheral blood DNA, cancer patient 88


title: peripheral-blood-dna_cancer-patient-87

description:
cancer patient peripheral blood
YP18

source_name: Peripheral blood DNA, cancer patient 87


title: 71990DCN


title: 71991CCAV

source_name: Cerebellar Cortex Anterior Vermis


title: peripheral-blood-dna_cancer-patient-86

description:
cancer patient peripheral blood
YP67

source_name: Peripheral blood DNA, cancer patient 86


title: peripheral-blood-dna_cancer-patient-95

description:
cancer patient peripheral blood
YP27

source_name: Peripheral blood DNA, cancer patient 95


title: 71990CCPV


title: 71990CCH


title: peripheral-blood-dna_cancer-patient-85

description:
cancer patient peripheral blood
YP50

source_name: Peripheral blood DNA, cancer patient 85


title: peripheral-blood-dna_cancer-patient-84

description:
cancer patient peripheral blood
YP34

source_name: Peripheral blood DNA, cancer patient 84


title: peripheral-blood-dna_cancer-patient-83

description:
cancer patient peripheral blood
YP26

source_name: Peripheral blood DNA, cancer patient 83


title: 71990CCAV


title: peripheral-blood-dna_cancer-patient-82

description:
cancer patient peripheral blood
YP24

source_name: Peripheral blood DNA, cancer patient 82


title: 71988DCN

source_name: Deep Cerebellar Nuclei


title: 71988CCPV


title: peripheral-blood-dna_cancer-patient-81

description:
cancer patient peripheral blood
YP58

source_name: Peripheral blood DNA, cancer patient 81


title: 71988CCH


title: peripheral-blood-dna_cancer-patient-79

description:
cancer patient peripheral blood
YP13

source_name: Peripheral blood DNA, cancer patient 79


title: peripheral-blood-dna_cancer-patient-80

description:
cancer patient peripheral blood
YP41

source_name: Peripheral blood DNA, cancer patient 80


title: 71988CCAV


title: peripheral-blood-dna_cancer-patient-78

description:
cancer patient peripheral blood
YP7

source_name: Peripheral blood DNA, cancer patient 78


title: 71987DCN


title: 71987CCPV

source_name: Cerebellar Cortex Posterior Vermis


title: 71987CCH


title: peripheral-blood-dna_cancer-patient-89

description:
cancer patient peripheral blood
YP15

source_name: Peripheral blood DNA, cancer patient 89


title: 71987CCAV


title: peripheral-blood-dna_cancer-patient-74

description:
cancer patient peripheral blood
X236

source_name: Peripheral blood DNA, cancer patient 74


title: peripheral-blood-dna_cancer-patient-76

description:
cancer patient peripheral blood
HCR019

source_name: Peripheral blood DNA, cancer patient 76


title: E14 retina-GDF15

city: Palo Alto

first: Ziming

last: Luo

state: CA

address: 1651 Pagemill Rd.

department: Ophthalmology

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
We applied fastp with the default parameters to filter the adaptor sequence and remove the low-quality reads to achieve clean data. Then the feature-barcode matrices were obtained by aligning reads to the mm10 genome using CellRanger v3.0.0.
Assembly: mm10
Supplementary files format and content: Barcodes and genes files (.tsv), and matrix files (.mtx).

source_name: E14 retina

extract_protocol:
Cells were dissociated using Accutase (Innovative Cell Technologies) for 15-20 minutes on day 5. Cell pellets were resuspended in PBS containing 0.04% bovine serum albumin and filtered through a 40μm cell strainer (Falcon, Cat#352340) to remove cell clumps. Cells were strained through the cell strainer and counted with a hemocytometer. 10,000 cells were then input into the 10X protocol. GEM generation, reverse transcription, cDNA amplification, and library construction steps were performed according to manufacturer’s instructions (Chromium Single Cell 3’v1/v2/v3 platform (10X Genomics, Pleasanton, CA).
Library construction steps were performed according to manufacturer’s instructions (Chromium Single Cell 3’v1/v2/v3 platform (10X Genomics, Pleasanton, CA).

value: E14 retina

tag: strain

value: Retinal neuron

value: wild-type


title: peripheral-blood-dna_cancer-patient-72

description:
cancer patient peripheral blood
X70

source_name: Peripheral blood DNA, cancer patient 72


title: peripheral-blood-dna_cancer-patient-73

description:
cancer patient peripheral blood
X173

source_name: Peripheral blood DNA, cancer patient 73


title: peripheral-blood-dna_cancer-patient-71

description:
cancer patient peripheral blood
A1127

source_name: Peripheral blood DNA, cancer patient 71


title: E14 retina-GDF11


title: E14 retina-PBS


title: AML12 cells, GEN202_23_87

city: Seville

first: Alejandro

last: Martin-Montalvo

address: Av/ Américo Vespucio 24

country: Spain

institute: CABIMER

description: control_vs_comparison.genes.deseq.countsAML12.csv

data_processing:
Quality control Analyses, FASTQ generation files, adapters trimming and filtering of sequencing were performed using the manufacturer’s software BaseSpace and followed by FASTQ toolkit v1.0.0
Assembly: Library UCSC mm10
Supplementary files format and content: The file includes raw counts for each sample

source_name: AML12 cells

growth_protocol:
AML12 cells cultured in DMEM/nutrient mixture F-12 Ham with 10 % fetal bovine serum, pen-strep, ITS Liquid Media Supplement, and 0.1 μM dexamethasone.
Wild-type male C57BL76 were fed with a standard healthy diet.

extract_protocol:
RNA extraction was performed using RNAeasy mini Kit (Qiagen)
RNA-seq libraries were made with the illumina stranded mRNA prep ligation kit following the corresponding user guide

treatment_protocol:
For AML12 cells: At 4 hours post-seeding cells were treated with siRNA Acly or control siRNA (Cultek). At 24 hours post siRNA interference cells were treated with Hydroxycitrate 1 mM, SB-204990 10 µM or Bempedoic acid 30 µM for 16 hours. Then samples were snap frozen.
Mice were injected or not with 10 µM cardiotoxin in the belly of the left hind limb. Then, mice were treated or not with hydroxycitrate fro 2 or 30 days. Gastrocnemius was harvested.

value: AML12 cells

value: Liver cells

value: siRNA Acly

value: Bempedoic acid


title: AML12 cells, GEN202_23_23


title: peripheral-blood-dna_cancer-patient-69

description:
cancer patient peripheral blood
MR0074

source_name: Peripheral blood DNA, cancer patient 69


title: AML12 cells, GEN202_23_22


title: peripheral-blood-dna_cancer-patient-67

description:
cancer patient peripheral blood
X206

source_name: Peripheral blood DNA, cancer patient 67


title: peripheral-blood-dna_cancer-patient-68

description:
cancer patient peripheral blood
BL143

source_name: Peripheral blood DNA, cancer patient 68


title: AML12 cells, GEN202_23_16


title: AML12 cells, GEN202_23_85


title: AML12 cells, GEN202_23_17


title: peripheral-blood-dna_cancer-patient-77

description:
cancer patient peripheral blood
YP42

source_name: Peripheral blood DNA, cancer patient 77


title: AML12 cells, GEN202_23_86

value: Hydroxycitrate


title: AML12 cells, GEN202_23_20


title: peripheral-blood-dna_cancer-patient-65

description:
cancer patient peripheral blood
X81

source_name: Peripheral blood DNA, cancer patient 65


title: peripheral-blood-dna_cancer-patient-64

description:
cancer patient peripheral blood
FH81

source_name: Peripheral blood DNA, cancer patient 64


title: peripheral-blood-dna_cancer-patient-63

description:
cancer patient peripheral blood
YP3

source_name: Peripheral blood DNA, cancer patient 63


title: AML12 cells, GEN202_23_19


title: AML12 cells, GEN202_23_15

value: No


title: peripheral-blood-dna_cancer-patient-75

description:
cancer patient peripheral blood
HCR005

source_name: Peripheral blood DNA, cancer patient 75


title: peripheral-blood-dna_cancer-patient-62

description:
cancer patient peripheral blood
MR0052

source_name: Peripheral blood DNA, cancer patient 62


title: AML12 cells, GEN202_23_14


title: peripheral-blood-dna_cancer-patient-61

description:
cancer patient peripheral blood
MR0016

source_name: Peripheral blood DNA, cancer patient 61


title: AML12 cells, GEN202_23_84


title: peripheral-blood-dna_cancer-patient-60

description:
cancer patient peripheral blood
MR0012

source_name: Peripheral blood DNA, cancer patient 60


title: peripheral-blood-dna_cancer-patient-70

description:
cancer patient peripheral blood
X219

source_name: Peripheral blood DNA, cancer patient 70


title: peripheral-blood-dna_cancer-patient-59

description:
cancer patient peripheral blood
LR0057

source_name: Peripheral blood DNA, cancer patient 59


title: AML12 cells, GEN202_23_83

value: siRNA control


title: AML12 cells, GEN202_23_11


title: peripheral-blood-dna_cancer-patient-58

description:
cancer patient peripheral blood
FH94

source_name: Peripheral blood DNA, cancer patient 58


title: AML12 cells, GEN202_23_10


title: peripheral-blood-dna_cancer-patient-57

description:
cancer patient peripheral blood
A1084

source_name: Peripheral blood DNA, cancer patient 57


title: peripheral-blood-dna_cancer-patient-56

description:
cancer patient peripheral blood
A1160

source_name: Peripheral blood DNA, cancer patient 56


title: peripheral-blood-dna_cancer-patient-66

description:
cancer patient peripheral blood
X80

source_name: Peripheral blood DNA, cancer patient 66


title: peripheral-blood-dna_cancer-patient-55

description:
cancer patient peripheral blood
A1085

source_name: Peripheral blood DNA, cancer patient 55


title: AML12 cells, GEN202_23_5

source_name: AML12 cells


title: peripheral-blood-dna_cancer-patient-53

description:
cancer patient peripheral blood
BS739

source_name: Peripheral blood DNA, cancer patient 53


title: AML12 cells, GEN202_23_4


title: AML12 cells, GEN202_23_82


title: peripheral-blood-dna_cancer-patient-52

description:
cancer patient peripheral blood
BL489

source_name: Peripheral blood DNA, cancer patient 52


title: peripheral-blood-dna_cancer-patient-50

description:
cancer patient peripheral blood
BL485

source_name: Peripheral blood DNA, cancer patient 50


title: peripheral-blood-dna_cancer-patient-51

description:
cancer patient peripheral blood
SG1269

source_name: Peripheral blood DNA, cancer patient 51


title: AML12 cells, GEN202_23_8


title: AML12 cells, GEN202_23_7


title: AML12 cells, GEN202_23_13


title: AML12 cells, GEN202_23_2


title: AML12 cells, GEN202_23_1


title: Gastrocnemius, GEN202_23_62

description: control_vs_comparison.genes.deseq.countsCTX.csv

source_name: Gastrocnemius

value: Gastrocnemius

value: Wild type

value: CTX-HC 30 days post injury


title: peripheral-blood-dna_cancer-patient-49

description:
cancer patient peripheral blood
BL368

source_name: Peripheral blood DNA, cancer patient 49

value: affected


title: peripheral-blood-dna_cancer-patient-48

description:
cancer patient peripheral blood
MR0046

source_name: Peripheral blood DNA, cancer patient 48


title: peripheral-blood-dna_cancer-patient-47

description:
cancer patient peripheral blood
HR0034

source_name: Peripheral blood DNA, cancer patient 47


title: Gastrocnemius, GEN202_23_61


title: peripheral-blood-dna_cancer-patient-46

description:
cancer patient peripheral blood
MR0042

source_name: Peripheral blood DNA, cancer patient 46


title: peripheral-blood-dna_cancer-patient-45

description:
cancer patient peripheral blood
MR0031

source_name: Peripheral blood DNA, cancer patient 45


title: Gastrocnemius, GEN202_23_63


title: peripheral-blood-dna_cancer-patient-43

description:
cancer patient peripheral blood
MR0077A

source_name: Peripheral blood DNA, cancer patient 43


title: Gastrocnemius, GEN202_23_50

value: CTX 30 days post injury


title: Gastrocnemius, GEN202_23_104


title: AML12 cells, GEN202_23_81


title: Gastrocnemius, GEN202_23_51


title: peripheral-blood-dna_cancer-patient-44

description:
cancer patient peripheral blood
LR0022

source_name: Peripheral blood DNA, cancer patient 44


title: peripheral-blood-dna_cancer-patient-54

description:
cancer patient peripheral blood
BS301

source_name: Peripheral blood DNA, cancer patient 54


title: peripheral-blood-dna_cancer-patient-42

description:
cancer patient peripheral blood
MR0049

source_name: Peripheral blood DNA, cancer patient 42


title: peripheral-blood-dna_cancer-patient-41

description:
cancer patient peripheral blood
MR0038

source_name: Peripheral blood DNA, cancer patient 41


title: peripheral-blood-dna_cancer-patient-40

description:
cancer patient peripheral blood
X216

source_name: Peripheral blood DNA, cancer patient 40


title: Gastrocnemius, GEN202_23_58

value: CTX-HC 2 days post injury


title: Gastrocnemius, GEN202_23_60


title: Gastrocnemius, GEN202_23_59


title: peripheral-blood-dna_cancer-patient-37

description:
cancer patient peripheral blood
X97

source_name: Peripheral blood DNA, cancer patient 37


title: peripheral-blood-dna_cancer-patient-39

description:
cancer patient peripheral blood
X69

source_name: Peripheral blood DNA, cancer patient 39


title: Gastrocnemius, GEN202_23_55

value: CTX 2 days post injury


title: peripheral-blood-dna_cancer-patient-38

description:
cancer patient peripheral blood
X84

source_name: Peripheral blood DNA, cancer patient 38


title: Gastrocnemius, GEN202_23_57


title: Gastrocnemius, GEN202_23_53


title: peripheral-blood-dna_cancer-patient-36

description:
cancer patient peripheral blood
X228

source_name: Peripheral blood DNA, cancer patient 36


title: peripheral-blood-dna_cancer-patient-34

description:
cancer patient peripheral blood
X85

source_name: Peripheral blood DNA, cancer patient 34


title: Gastrocnemius, GEN202_23_107

source_name: Gastrocnemius


title: peripheral-blood-dna_cancer-patient-35

description:
cancer patient peripheral blood
X210

source_name: Peripheral blood DNA, cancer patient 35


title: peripheral-blood-dna_cancer-patient-33

description:
cancer patient peripheral blood
X88

source_name: Peripheral blood DNA, cancer patient 33


title: Gastrocnemius, GEN202_23_54


title: Gastrocnemius, GEN202_23_56


title: peripheral-blood-dna_cancer-patient-32

description:
cancer patient peripheral blood
X223

source_name: Peripheral blood DNA, cancer patient 32


title: wt3

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

data_processing:
Sequence reads were mapped to the GRCm39 mouse genome build using STAR v. 2.7.10a
Counts for each transcript were collected using featureCounts from Subread package (v. 2.0.1),  with options -Q 10 -p -B -C -s 2 -g gene_id -t exon and Gencode vM26 annotation.
Differential expression analysis was performed using DESeq2.
Assembly: GRCm39
Supplementary files format and content: Processed data file contains DESEq2-normalized counts for each sample in the csv format

source_name: oocytes

growth_protocol: Mice were bred in the animal house of the Faculty of Biology, University of Warsaw, and maintained under conventional conditions24,25,30 in open polypropylene cages filled with wood chip bedding enriched with nest material and paper tubes. Mice were fed at libutum with a standard laboratory diet (Labofeed B, Morawski). Humidity in the rooms was kept at 55 ± 10%, the temperature at 22 °C ± 2 °C, at  least 15 air changes per hour, and the light regime set at 12 h/12 h (lights on from 6:00 to 18:00). Health monitoring was performed regularly at the IDEXX laboratory.

extract_protocol:
Total RNA from oocytes was isolated using PicoPure RNA isolation kit (Thermo Fischer Scientific, Cat# KIT0204) according to manufacturer's protocol with following adjustments: groups of isolated oocytes were placed in 10 µl of provided Extraction Buffer in PCR tubes and incubated for 30 min in 42 °C on thermoblock. Samples were then stored in –80 °C. Before proceeding to next step, samples were pooled for total of 30 oocytes per sample and amount of provided ethanol used was adjusted depending on final sample volume. RNA was eluted with 11 µl of Elution Buffer provided. DNA was removed from final sample by DNase treatment using TURBO DNA-free Kit (Thermo Fisher Scientific, Cat# AM1907) according to manufacturer's protocol. DNA-free RNA was stored in –80 °C.
cDNA was produced using SuperScript III reverse transcriptase (Thermo Fisher Scientific, Cat# 18080093) according to manufacturers protocol with oligo(dT) priming and addition of ERCC RNA Spike-InMix (final dilution: 1:100000; Life Technologies, Cat# 4456740) for first-strand synthesis from oocyte-isolated RNA and RiboLock RNase inhibitor (40 units; Thermo Fischer Scientific, Cat# EO0382) for second strand synthesis in all samples. Output material was purified in 1 volume of AMPure XP beads, eluted in 20 µl nuclease-free water and second strand synthesis reaction was set up by addition of following components: Second Strand Buffer (NEB, Cat# B6117S), RNase H (10 units; NEB, Cat# M0297S), E. coli DNA ligase (10 units; NEB, Cat# M0205S), E. coli DNA polymerase (50 units), dNTPs (final conc. 0.4 mM) and nuclease-free water for a final reaction volume of 50 µl. Reaction was incubated in 16oC overnight. Final cDNA output was purified in 1 volume AMPure XP beads and eluted with 10 µl of nuclease-free water. Tagmentation reaction was performed following published protocols63,64 with various steps and amount of enzyme used optimized for use of homemade batch of Tn5 transposase produced in our laboratory. Briefly: 100 µM Tn5ME-A and Tn5ME-B oligonucleotides in annealing buffer (50 mM NaCl, 40 mM Tris-HCl pH = 8) were mixed 1:1 with 100 mM Tn5MErev oligonucleotide and incubated in thermocycler in 95°C for 5 min and 65°C for 5 min, and finaly cooled to 4oC and stored at -20 oC (with slow cooling between each step). Tn5 (0.25 mg/ml) was loaded with linker oliguncleotides Tn5ME-A/Tn5MErev and Tn5ME-B/Tn5MErev (see Supplemental Table 1 for full sequences) by mixing of 10 µl Tn5 with 0.5 µl of both linkers (0.35 µM) and incubating for 45 min in 23oC with shaking at 350 rpm. Right before the reaction setup loaded Tn5 was diluted 10 times with nuclease-free water. 10 µl of freshly prepared tagmentation buffer (20mM Tris-HCl ph 7.5; 20  mM MgCl2; 50 % dimethylformamid)  were mixed with 5 µl of diluted Tn5 and 5 µl od cDNA, incubated for 3 min at 55oC in preheated thermocycler and cooled to 10oC for 1 min. Reaction was inactivated by addition of 5 µl 0,2% SDS and incubation for 5 min at RT. Tagmented cDNA was purified in 1.25 volume of AMPure XP beads and eluted in 10 µl of nuclease-free water. For library amplification KAPA HiFi HotStart ReadyMix 2x (Roche, Cat# KK2602) with addition of 5% DMSO was used. 5 µl of tagmented cDNA was used for 15 µl reaction volume. Reaction was run in thermocycler with following program: 72oC – 15 min., 95oC – 30 s., 15 cycles: (98oC – 20s., 58oC – 15s., 72o – 30s.), 72oC – 3 min., 4oC - hold. Number of cycles yielding best results was determined experimentally and was further individually adjusted for each batch of prepared cDNA.

treatment_protocol: no

value: oocytes

value: wild type

tag: Sex

value: female


title: wt2

description: Processed data file contains DESEq2-normalized counts for each sample in the csv format


title: peripheral-blood-dna_cancer-patient-31

description:
cancer patient peripheral blood
X161

source_name: Peripheral blood DNA, cancer patient 31


title: peripheral-blood-dna_cancer-patient-30

description:
cancer patient peripheral blood
X83

source_name: Peripheral blood DNA, cancer patient 30


title: peripheral-blood-dna_cancer-patient-29

description:
cancer patient peripheral blood
FH93

source_name: Peripheral blood DNA, cancer patient 29


title: peripheral-blood-dna_cancer-patient-28

description:
cancer patient peripheral blood
FH88

source_name: Peripheral blood DNA, cancer patient 28


title: wt1


title: BC1

value: Tent5b-/- Tent5c-/-


title: BC2


title: peripheral-blood-dna_cancer-patient-27

description:
cancer patient peripheral blood
FH84

source_name: Peripheral blood DNA, cancer patient 27


title: Young MRL-lpr kidney

city: Seoul

first: Hye Young

last: Kim

address: 103 Daehak-ro, Jongro-gu

country: South Korea

institute: Seoul National University

data_processing:
Samples were sequenced paired-end 100bp by Illumina NovaSeq 6000 platform and preliminary sequencing results were converted to FASTQ files with Cell Ranger v3
The 10x Genomics standard seq protocol by trimming the barcode and unique molecular identifier (UMI) end to 28 bp, and the mRNA end to 91 bp.
The FASTQ files were aligned to the mouse reference genome (mm10).
Quality control of the processed expression matrix were performed by evaluating detected transcripts, detected counts, cell doublets, mito-ratio.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files for each samples.

source_name: Kidney

extract_protocol:
(scRNA-Seq has nothing to do with this step)
Library construction was performed using the 10X Chromium Single Cell 3’ Reagent Kits v3.1.

value: Kidney

tag: age

value: young

value: MRL-lpr


title: peripheral-blood-dna_cancer-patient-26

description:
cancer patient peripheral blood
FH90

source_name: Peripheral blood DNA, cancer patient 26


title: Old MRL-lpr kidney

value: old


title: Soleo_HCA, rep4

description:
GEN_52_21_78
SoleoSTD_vs_SoleoSTDHCA.genes.deseq.counts
DEseq_Soleo_STDvHCA

data_processing:
The reads were mapped to the mouse genome (mouse-UCSC : M.musculus-UCSC-mm10) RNA-Seq Alignment Illumina  Version: 2.0.2
DEseq analysis using the application RNA-Seq Differential Expression  Illumina Version: 1.0.1
Assembly: mm10
Supplementary files format and content: Counts .Xlsx file format (data delimited by ",")
Supplementary files format and content: DEseq .Xlsx file format (data delimited by ",")

source_name: Soleo

extract_protocol:
RNAeasy mini Kit (Qiagen).
NEBNext rRNA Depletetion and NEBNext Ultra II directional RNA library prep kit for Illumina

value: Soleo

value: Hydroxycitrate (HC)


title: peripheral-blood-dna_cancer-patient-25

description:
cancer patient peripheral blood
FH96

source_name: Peripheral blood DNA, cancer patient 25


title: Soleo_HCA, rep5

description:
GEN_52_21_79
SoleoSTD_vs_SoleoSTDHCA.genes.deseq.counts
DEseq_Soleo_STDvHCA


title: peripheral-blood-dna_cancer-patient-22

description:
cancer patient peripheral blood
FH95

source_name: Peripheral blood DNA, cancer patient 22


title: peripheral-blood-dna_cancer-patient-24

description:
cancer patient peripheral blood
FH91

source_name: Peripheral blood DNA, cancer patient 24


title: Soleo_HCA, rep3

description:
GEN_52_21_77
SoleoSTD_vs_SoleoSTDHCA.genes.deseq.counts
DEseq_Soleo_STDvHCA


title: Soleo_HCA, rep2

description:
GEN_52_21_76
SoleoSTD_vs_SoleoSTDHCA.genes.deseq.counts
DEseq_Soleo_STDvHCA


title: peripheral-blood-dna_cancer-patient-20

description:
cancer patient peripheral blood
YP53

source_name: Peripheral blood DNA, cancer patient 20


title: Soleo_HCA, rep1

description:
GEN_52_21_75
SoleoSTD_vs_SoleoSTDHCA.genes.deseq.counts
DEseq_Soleo_STDvHCA


title: Soleo_STD, rep5

description:
GEN_52_21_74
SoleoSTD_vs_SoleoSTDHCA.genes.deseq.counts
DEseq_Soleo_STDvHCA

value: Standard (STD)


title: peripheral-blood-dna_cancer-patient-19

description:
cancer patient peripheral blood
YP45

source_name: Peripheral blood DNA, cancer patient 19


title: peripheral-blood-dna_cancer-patient-18

description:
cancer patient peripheral blood
YP51

source_name: Peripheral blood DNA, cancer patient 18


title: Soleo_STD, rep3

description:
GEN_52_21_72
SoleoSTD_vs_SoleoSTDHCA.genes.deseq.counts
DEseq_Soleo_STDvHCA


title: Soleo_STD, rep2

description:
GEN_52_21_71
SoleoSTD_vs_SoleoSTDHCA.genes.deseq.counts
DEseq_Soleo_STDvHCA


title: peripheral-blood-dna_cancer-patient-16

description:
cancer patient peripheral blood
YP54

source_name: Peripheral blood DNA, cancer patient 16


title: Soleo_STD, rep4

description:
GEN_52_21_73
SoleoSTD_vs_SoleoSTDHCA.genes.deseq.counts
DEseq_Soleo_STDvHCA


title: Soleo_STD, rep1

description:
GEN_52_21_70
SoleoSTD_vs_SoleoSTDHCA.genes.deseq.counts
DEseq_Soleo_STDvHCA


title: peripheral-blood-dna_cancer-patient-17

description:
cancer patient peripheral blood
YP4

source_name: Peripheral blood DNA, cancer patient 17


title: Liver_HCA, rep5

description:
GEN_52_21_10
STD_vs_LiverSTDvsHCA.genes.deseq.counts
DEseq_Liver_STDvHCA

source_name: Liver

value: Liver


title: peripheral-blood-dna_cancer-patient-15

description:
cancer patient peripheral blood
YP52

source_name: Peripheral blood DNA, cancer patient 15


title: peripheral-blood-dna_cancer-patient-14

description:
cancer patient peripheral blood
YP66

source_name: Peripheral blood DNA, cancer patient 14


title: Liver_HCA, rep2

description:
GEN_52_21_7
STD_vs_LiverSTDvsHCA.genes.deseq.counts
DEseq_Liver_STDvHCA


title: Liver_HCA, rep3

description:
GEN_52_21_8
STD_vs_LiverSTDvsHCA.genes.deseq.counts
DEseq_Liver_STDvHCA


title: peripheral-blood-dna_cancer-patient-13

description:
cancer patient peripheral blood
YP36

source_name: Peripheral blood DNA, cancer patient 13


title: peripheral-blood-dna_cancer-patient-12

description:
cancer patient peripheral blood
YP64

source_name: Peripheral blood DNA, cancer patient 12


title: Liver_HCA, rep4

description:
GEN_52_21_9
STD_vs_LiverSTDvsHCA.genes.deseq.counts
DEseq_Liver_STDvHCA


title: Liver_HCA, rep1

description:
GEN_52_21_6
STD_vs_LiverSTDvsHCA.genes.deseq.counts
DEseq_Liver_STDvHCA


title: peripheral-blood-dna_cancer-patient-10

description:
cancer patient peripheral blood
YP10

source_name: Peripheral blood DNA, cancer patient 10


title: Liver_STD, rep5

description:
GEN_52_21_5
STD_vs_LiverSTDvsHCA.genes.deseq.counts
DEseq_Liver_STDvHCA


title: peripheral-blood-dna_cancer-patient-21

description:
cancer patient peripheral blood
YP12

source_name: Peripheral blood DNA, cancer patient 21


title: peripheral-blood-dna_cancer-patient-23

description:
cancer patient peripheral blood
FH89

source_name: Peripheral blood DNA, cancer patient 23


title: Liver_STD, rep4

description:
GEN_52_21_4
STD_vs_LiverSTDvsHCA.genes.deseq.counts
DEseq_Liver_STDvHCA


title: peripheral-blood-dna_cancer-patient-9

description:
cancer patient peripheral blood
YP49

source_name: Peripheral blood DNA, cancer patient 9


title: Liver_STD, rep3

description:
GEN_52_21_3
STD_vs_LiverSTDvsHCA.genes.deseq.counts
DEseq_Liver_STDvHCA


title: Liver_STD, rep2

description:
GEN_52_21_2
STD_vs_LiverSTDvsHCA.genes.deseq.counts
DEseq_Liver_STDvHCA


title: ACLi_TGFb_C18

city: Philadelphia

first: Michael

middle: Panagiotis

last: Lazaropoulos

state: PA

address: 3500 North Broad Street

department: Department of Cardiovascular Sciences

institute: Temple University

data_processing:
library strategy: CUT&RUN
fastq files were returned as paired-end 150 base pair reads
H3K27ac CUT&RUN data were processed using CUT-RUNTools-2.0 (executes adapter trimming, read alignment, duplicate marking, peak calling, and blacklist filtering).
adapter trimming using Trimmomatic and align reads to the mm10 genome at an 85-95% alignment rate using bowtie2
peak calling was performed for each sample using the MACS2 callpeak function with -q 0.01 as a parameter to retain only peaks passing our statistical threshold of q<0.01.
DiffBind version 3.2.7 was used to generate a list of consensus peaks measured in at least 4 samples across the experiment (dba.count() with minOverlap=4), and statistically test for differential binding between biological conditions
Deduped .bam files and blacklist filtered peak files were used as inputs for DiffBind, and differentially occupied peaks were classified as those passing FDR<0.05.
Assembly: mm10
Supplementary files format and content: bigWig, BED

source_name: primary cardiac fibroblasts

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin, 1x non-essential amino acids. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cardiac fibroblasts were fixed with 0.1% formaldehyde for 1 minute, followed by quenching with 125mM glycine. After, chromatin was isolated according to protocol from Eipcypher Kit: 14-1048, with 0.01% digitonin to permeabilize cells.
CUTANA™ CUT&RUN Library Prep Kit (14-1001) following manufacterers instructions. 5ng CUT&RUN enriched DNA was used as starting material for IP samples. Libraries were amplified using 14 cycles on the thermocycler. Libraries checked with Qubit for quantification and bioanalyzer for size distribution at Novogene.

treatment_protocol: DMEM, 1% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin, 1x non-essential amino acids. Cells were cultured at 37C at 5% CO2. Treated with or without 10ng/mL TGFβ and with ACLY inhibitor (4µM BMS-303141) or DMSO.

tag: group

value: primary cardiac fibroblasts

value: H3K27ac (Epicypher, 13-0045)


title: peripheral-blood-dna_cancer-patient-4

description:
cancer patient peripheral blood
HCR020

source_name: Peripheral blood DNA, cancer patient 4

value: affected


title: peripheral-blood-dna_cancer-patient-3

description:
cancer patient peripheral blood
HCR017

source_name: Peripheral blood DNA, cancer patient 3


title: TGFb_D14

value: TGFb


title: peripheral-blood-dna_cancer-patient-1

description:
cancer patient peripheral blood
HCR007

source_name: Peripheral blood DNA, cancer patient 1


title: peripheral-blood-dna_cancer-patient-11

description:
cancer patient peripheral blood
YP40

source_name: Peripheral blood DNA, cancer patient 11


title: dRNA-seq_WT_-TEX_R1

city: Würzburg

first: Cynthia

last: Sharma

state: Bavaria

address: Josef-Schneider-Straße 2

country: Germany

institute: University of Würzburg

data_processing:
Demultiplexing
FASTQ-format reads were trimmed with a cutoff Phred score of 20 using Cutadapt (version: 4.1) (Martin, 2011).
After poly(A)‐tails were removed, sequences shorter than 12 nt were omitted and the remaining reads mapped to the C. jejuni NCTC11168 reference genome (NCBI accession number: NC_002163.1, RefSeq assembly accession number: GCF_000009085.1) using READemption (version: 2.0.1) (Förstner et al., 2014) and segemehl (version: 0.3.4) (Hoffmann et al., 2009) with an accuracy cutoff of 95%.
Coverage plots containing the number of mapped reads per nucleotide were also generated with READemption and visualized in the Integrated Genome Browser (Freese et al., 2016). The coverage was normalized by the total number of aligned reads of a given library and multiplied by the minimum number of aligned reads calculated over all libraries.
Assembly: ASM908v1
Supplementary files format and content: normalized read coverages in wiggle format with full-length alignment based read coverage (*_forward.wig = plus strand; *_reverse.wig = minus strand)

organism: Campylobacter jejuni

source_name: bacteria

growth_protocol: Bacteria were grown in Brucella Broth (supplemented with 10 µg/ml vancomycin) at 37°C in a microaerobic atmosphere (10% CO2, 5% O2) until log phase.

extract_protocol:
total RNA was treated with DNase I to digest genomic DNA, terminator exonuclease treatment of one half of each RNA sample
small RNA protocol, as previously described (Berezikov et al., 2006), but without RNA fractionation prior to cDNA synthesis: Equal amounts of RNA were poly(A)‐tailed using poly(A) polymerase and 5’-triphosphate groups were digested with tobacco acid pyrophosphatase (TAP). Then, an RNA adapter was ligated to the 5’ phosphate and first‑strand cDNA synthesised with an oligo(dT)‐adapter primer and M‑MLV (Moloney Murine Leukaemia Virus) reverse transcriptase. A high-fidelity DNA polymerase was used to PCR‐amplify the resulting cDNA to a concentration of ~20‐30 ng/μl. Finally, cDNA was purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis.

value: bacteria

value: wildtype

value: untreated


title: peripheral-blood-dna_cancer-patient-8

description:
cancer patient peripheral blood
YP39

source_name: Peripheral blood DNA, cancer patient 8


title: dRNA-seq_WT_+TEX_R1

value: terminator exonuclease


title: peripheral-blood-dna_cancer-patient-6

description:
cancer patient peripheral blood
YP1

source_name: Peripheral blood DNA, cancer patient 6


title: peripheral-blood-dna_cancer-patient-2

description:
cancer patient peripheral blood
HCR014

source_name: Peripheral blood DNA, cancer patient 2


title: peripheral-blood-dna_cancer-patient-7

description:
cancer patient peripheral blood
YP65

source_name: Peripheral blood DNA, cancer patient 7


title: ACLi_TGFb_B17


title: ACLi_C8

value: ACLi


title: ACLi_TGFb_D19


title: PC12-EN1, miRNA-seq

city: Zhengzhou

first: Jinsheng

last: Huang

address: 1th, East Jianshe Road

institute: Zhengzhou University

data_processing:
Illumina Casava2.19 software used for basecalling.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rnor_6.0 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Rnor_6.0
Supplementary files format and content: Matrix table with raw counts for every miRNA and every sample

organism: Rattus norvegicus

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: rat adrenal pheochromocytoma cells

value: EN


title: peripheral-blood-dna_cancer-patient-5

description:
cancer patient peripheral blood
HCR021

source_name: Peripheral blood DNA, cancer patient 5


title: ACLi_D9


title: TGFb_C13


title: PC12-EN2, miRNA-seq


title: PC12-EN3, miRNA-seq


title: PC12-EC2, miRNA-seq

value: EC


title: ACLi_A6


title: TGFb_B12


title: dRNA-seq_∆rnc_-TEX_R1

value: deltarnc


title: ctrl_C3

value: ctrl


title: Liver_STD, rep1

description:
GEN_52_21_1
STD_vs_LiverSTDvsHCA.genes.deseq.counts
DEseq_Liver_STDvHCA

source_name: Liver


title: dRNA-seq_∆rnc_+TEX_R1


title: ctrl_A1


title: sample_270: Liver from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software by the sequencing service provider.
Raw reads were processed for quality control using fqC v0.11.5 and TrimGalore! software v0.6.4_dev. This software was used to trim low-quality ends from reads, for Illumina adapter removal, and for removal of excess poly(A)-tails.
STAR v2.7.7a was used for alignment of reads to the rainbow trout genome using the default alignment parameters recommended by the STAR software.
Gene counts for reverse-stranded preparations were provided by STAR v2.7.7a using default parameters recommended by the STAR software.
Read counts output from the STAR v2.7.7a software were used to calculate fold-change using the DESeq2 package 1.24.0 in R-BiocManager Release 1.30.10.
Genome_build: All unmasked sequences from the rainbow trout primary assembly in Ensemble (Oncorhynchus_mykiss.Omyk_1.0.dna.primary_assembly)
Supplementary_files_format_and_content: Tab-delimited text files of effective read counts, rounded to the nearest whole number

molecule: polyA RNA

organism: Oncorhynchus mykiss

extract_protocol:
Tissue samples were placed in RNAlater and stored at -80°C until usage. Total RNA was extracted with the Qiagen RNeasy Mini Kit per the manufacturer's recommendation. Total RNA was treated with Amplification Grade DNase I from Sigma-Aldrich and then precipitated prior to library construction.
Library for RNA-Seq was prepared according to KAPA Stranded mRNA-Seq poly-A selected kit with 200-300bp insert size (KAPA Biosystems, Wilmington, MA) using 250 ng total RNAs as input. Final library quality and quantity was analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit 3.0 Fluorometer. The RNA integrity was checked by Agilent Bioanalyzer 2100 and samples with clean rRNA peaks were used for further experiments.
RNA-Seq of 150 bp PE (paired end) reads were sequenced on Illumina HiSeq 4000 (Illumina Inc., San Diego, CA).

tag: FISH strain

value: PSel

tag: pathogen strain

value: IHNV

tag: time post pathogen challenge

value: 48 hrs


title: PC12-EC3, miRNA-seq


title: ctrl_B2

value: primary cardiac fibroblasts


title: ACLi_B7

value: H3K27ac (Epicypher, 13-0045)


title: PC12-EN2

data_processing:
Illumina Casava2.19 software used for basecalling.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rnor_6.0 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Rnor_6.0
Supplementary files format and content: Matrix table with raw counts for every gene and every sample


title: PC12-EN3


title: ctrl_D4


title: PC12-EN1


title: sample_267: Liver from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge

value: Liver


title: PC12-EC3


title: sample_266: Liver from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: PC12-EC2


title: PC12-EC1


title: sample_265: Liver from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_264: Intestine from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge

source_name: Intestine

value: Intestine


title: PC12-EC1, miRNA-seq


title: CPE3

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

institute: Hanyang Univ.

data_processing:
Illumina CASAVA v1.8.2 software was used for base calling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
Quality controlled FASTQ files were alignment to Mus musculus UCSC rn6 reference genome sequence using the STAR (version 2.5.1) aligner software. To measure differential gene expression, DESeq2 was used.
The number of reads mapped to gene ID features were counted using STAR.
Assembly: Rattus norvegicus UCSC rn6
Supplementary files format and content: tab-delimited text files including normalized read counts for each sample

source_name: rat pXEN cells RX1

growth_protocol: The plates were coated with 10 µg/ml Collagen I (“Coll1”) and the cells were kept in DMEM/F12 supplemented with Neurobasal, N2 supplement, B27 supplement, and β-mercaptoethanol, plus Chir99021 (1 µM), Pdgf (10 ng/ml), and Egf  (10 ng/ml).

extract_protocol:
RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. For RNA-Seq, RNA libraries were created from each group using the NEBNext® Ultra™ Directional RNA Library preparation kit from Illumina® (Illumina, San Diego, CA, USA). The first step in the workflow involved the removal of ribosomal RNA using the RNAMius™ Transcriptome Isolation kit (Life Technologies, Carlsbad, CA, USA).  Following purification, total RNA was fragmented into small pieces using divalent cations at elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments were then processed through an end-repair reaction by the addition of a single ‘A’ base, followed by ligation of the adapters. The products of these reactions were then purified and enriched by PCR to create the final cDNA library. The cDNA fragments were sequenced using the Illumina HiSeq2000 (101 cycles PE lane)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth medium

value: cultured in serum-free medium containing Chir99021

value: WKY


title: sample_263: Intestine from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: CPE2


title: sample_262: Intestine from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: LPE2

growth_protocol: The plates were coated with 10 µg/ml Collagen I (“Coll1”) and the cells were kept in DMEM/F12 supplemented with Neurobasal, N2 supplement, B27 supplement, and β-mercaptoethanol, plus Lif (10 ng/ml), Pdgf (10 ng/ml), and Egf  (10 ng/ml).

value: cultured in serum-free medium containing Lif


title: TGFb_A11

value: TGFb


title: LPE3


title: CPE1


title: sample_260: Intestine from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_259: Intestine from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_269: Liver from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_261: Intestine from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_268: Liver from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_258: Kidney from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge

source_name: Kidney

value: Kidney


title: T3

growth_protocol: The cells were kept on Fibronectin (100 ng/ml)-coated plates (condition denoted as “FNlo”) in DMEM/ MCDB medium supplemented with LA-BSA, ITS, L-ascorbic acid, β-mercaptoethanol, 2% (v/v) FBS, 0.5 μM Dexamethasone, 10 ng/ml Pdgf, 10 ng/ml Egf, and 10 ng/ml Lif

value: cultured in traditional serum medium


title: T2


title: sample_257: Kidney from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_256: Kidney from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: Lungs TMZ_4

city: Toyama

first: Jun-Dal

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

data_processing: Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.

source_name: TMZ

extract_protocol:
Tissue-derived total RNA was prepared according to the manufacturer’s protocol of ISOGEN plus (TAKARA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Male Sprague Dawley rats (SLC, Japan), 130–150 g, were dosed subcutaneously with 20 mg/kg SU-5416 and exposed to 3 weeks of hypoxia (10% oxygen) following 2 weeks of normoxia. Rats were then administered vehicle or chrysin (100 mg/kg/day) or TMZ (0.7 g/L drinking water) for 3 weeks under normoxic conditions (SU_HX group, Chrysin group, TMZ group, respectively). Control rats were maintained in normoxic conditions for 8 weeks (CTRL group).

value: Sprague Dawley

value: Lung

tag: age & sex

value: 5-week-old, Male

value: SU_HX_Trimetazidine  treatment (TMZ), hypoxic conditions


title: sample_255: Kidney from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge

value: PSel


title: sample_254: Kidney from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge

value: IHNV


title: Lungs TMZ_3


title: sample_253: Kidney from PSel strain fish exposed to IHNV at timepoint 48 hrs post challenge

value: 48 hrs


title: Lungs TMZ_2


title: Lungs TMZ_1


title: sample_251: Liver from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: 24 hrs


title: LPE1


title: Lungs Chrysin_2

source_name: Chrysin

value: SU_HX_Chrysin treatment (Chrysin), hypoxic conditions


title: Lungs Chrysin_4


title: Lungs Chrysin_3


title: sample_250: Liver from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: Liver


title: sample_248: Liver from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_249: Liver from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_245: Intestine from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: Intestine


title: Lungs SU_HX_4

value: Sugen treatment (SU_HX), hypoxic conditions


title: T1

value: WKY


title: sample_246: Intestine from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_244: Intestine from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: Lungs SU_HX_1


title: sample_243: Intestine from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: Lungs Chrysin_1


title: Lungs SU_HX_3


title: sample_242: Intestine from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: Lungs CTRL_4

source_name: Control

value: Control (CTRL), normoxic conditions


title: Lungs CTRL_2


title: Lungs SU_HX_2


title: Lungs CTRL_3


title: Lungs CTRL_1


title: sample_252: Liver from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_239: Kidney from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_238: Kidney from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_237: Kidney from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_247: Liver from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_236: Kidney from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_234: Liver from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: 12 hrs


title: Perianal14_Fistula_cytoRNA

city: New York

first: Judy

last: Cho

state: NY

address: 1470 Madison Avenue, 8th Fl., Box 1498;

department: Pathology, Molecular and Cell-Based Medicine

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

data_processing:
Single Cell Process Illumina sequencing products were demultiplexed by the University of Minnesota Genomic Center (UMGC). Prepared FASTQ files were fed into the cellranger count v6.1.1 pipeline for additional QC, alignment, and matrices generation. Filtered matrix outputs were brought into the Seurat wrapper, coreSC, for broad-scope data cleaning and regularization. Gene expression variance stabilization was conducted using the SCTransform v2 function. Normalized GEX outputs were passed to principal component analysis (PCA) and uniform manifold projection (UMAP) for dimensionality reduction and 2-dimensional projection. Individual samples were combined into a single, integrated object and harmonized for batch effects using the Harmony package. Clusters were annotated by parallel data driven and known marker approaches and validated with CellTypist. Clusters classified as myeloid or stromal were subset from the larger Seurat object and sub-clustered.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: MEX compatible cell-associated barcodes list
Supplementary files format and content: MEX compatible gene ID/name list
Supplementary files format and content: MEX format feature-barcode associated UMI count sparse matrix

molecule: cytoplasmic RNA

source_name: fistula tract lining biopsies

extract_protocol:
Single Cell Sampling and Isolation  Biopsies for single cell processing were obtained from patients at the time of colonoscopy or upon undergoing abdominoperineal resection (completion proctectomy). At endoscopy, ~4 biopsies per region were collected by the physician for further single cell isolation. From proctectomy specimens, 10-20 biopsies per region were collected by the researcher using an endoscopic forceps prior to pathological grossing. To sample the fistula tract, a cross-section was first excised and then transected to expose the tract lining and facilitate biopsy acquisition. From surgical specimens with patent perianal fistulas, cross sections of the tract were resected with the assistance of the pathologist or pathology PA and preserved in O.C.T. Compound (Sakura) by the Mount Sinai Biorepository Core. FFPE specimens were retrieved from clinical samples previously processed and banked by the Biorepository.  Single cell suspensions were prepared from 4-10 biopsies as previously described21. If cell viability was < 70%, dead cells were depleted using the Dead Cell Removal Kit (Miltenyi, cat.no. 130-090-101). Single cells were loaded onto the 10X Chromium Controller at a targeted concentration of 6000 cells/lane, using the Chromium 3’ v3.1 chemistry (PN-1000121), per manufacturer instructions.
Cells were loaded on a Chromium Next GEM Chip G Single Cell Kit (PN-1000127) with GEMs from the Chromium Next GEM Single Cell 3’ Kit v3.1 (PN-1000268) and indexed using the Dual Index Kit TT Set A (PN-1000215) according to 10x protocol CG000315 Revs B,C.

value: fistula tract lining biopsies

tag: procedure

value: proctectomy


title: Perianal12_Rect_cytoRNA

description: 10x Genomics

source_name: rectum biopsies

value: rectum biopsies

value: colonoscopy


title: Perianal14_Rect_cytoRNA

description: 10x Genomics


title: Perianal13_Sig_cytoRNA

description: 10x Genomics

source_name: sigmoid colon biopsies

value: sigmoid colon biopsies


title: sample_241: Intestine from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: Perianal12_Sig_cytoRNA

description: 10x Genomics


title: sample_231: Liver from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: Perianal10_Sig_cytoRNA

description: 10x Genomics


title: sample_230: Liver from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: Perianal10_Rect_cytoRNA

description: 10x Genomics


title: Perianal11_Fistula_cytoRNA

description: 10x Genomics


title: Perianal11_Rect_cytoRNA

description: 10x Genomics


title: sample_240: Kidney from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: Kidney


title: Perianal9_Rect_cytoRNA

description: 10x Genomics


title: sample_227: Intestine from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: PSel


title: Perianal9_Sig_cytoRNA

description: 10x Genomics


title: sample_233: Liver from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: IHNV


title: Perianal8_Sig_cytoRNA

description: 10x Genomics


title: sample_228: Intestine from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: sample_226: Intestine from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: sample_225: Intestine from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: Perianal13_Rect_cytoRNA

description: 10x Genomics


title: sample_235: Kidney from PSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: Perianal7_Sig_cytoRNA

description: 10x Genomics


title: sample_224: Intestine from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: Perianal7_Rect_cytoRNA

description: 10x Genomics


title: sample_232: Liver from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: sample_223: Intestine from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: Perianal6_Sig_cytoRNA

description: 10x Genomics


title: sample_229: Liver from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: sample_222: Kidney from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: sample_221: Kidney from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: sample_220: Kidney from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: Perianal6_Rect_cytoRNA

description: 10x Genomics


title: Perianal5_Sig_cytoRNA

description: 10x Genomics


title: sample_218: Kidney from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: Perianal5_Rect_cytoRNA

description: 10x Genomics


title: sample_217: Kidney from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: Perianal4_TI_cytoRNA

description: 10x Genomics

source_name: terminal ileum biopsies

value: terminal ileum biopsies


title: Perianal4_Rect_cytoRNA

description: 10x Genomics


title: sample_219: Kidney from PSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: sample_215: Liver from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: 4 hrs


title: sample_216: Liver from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: sample_214: Liver from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: Perianal3_Sig_cytoRNA_R

description: 10x Genomics


title: Perianal2_Sig_cytoRNA_R

description: 10x Genomics


title: sample_213: Liver from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: Perianal2_Rect_cytoRNA_R

description: 10x Genomics


title: Perianal8_Rect_cytoRNA

description: 10x Genomics


title: Perianal3_Sig_cytoRNA

description: 10x Genomics


title: Perianal3_Rect_cytoRNA_R

description: 10x Genomics


title: sample_212: Liver from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: sample_211: Liver from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: Perianal2_Sig_cytoRNA

description: 10x Genomics


title: Perianal3_Rect_cytoRNA

description: 10x Genomics


title: sample_210: Intestine from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: Perianal2_Rect_cytoRNA

description: 10x Genomics


title: sample_209: Intestine from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: Perianal1_Sig_cytoRNA

description: extracted 10x GEX modality from TotalSeq

value: colectomy


title: sample_207: Intestine from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: Perianal13_Sig_nuATAC

library_source: other

data_processing:
Multiome data processing  Illumina sequencing products were demultiplexed by the University of Minnesota Genomic Center (UMGC) using the cellranger arc demux v2.0.0 pipeline with default parameters. FASTQ files were assessed for quality with UMGC's internal toolset, gopher-pipelines v2.2 consisting notably of fastqc v0.11.7,  samtools v1.9, and trimmomatic v0.33. Additional QC was performed during alignment with the cellranger arc count v2.0.0 tool. Cellranger outputs were then carried into Seurat for regularization and modality integration. Gene expression variance stabilization was conducted using the SCTransform v2 function. Normalized GEX outputs were passed to principal component analysis (PCA) and uniform manifold projection (UMAP) for dimensionality reduction and 2-dimensional projection. Neighborhood formation was performed with combined, weighted values of both modalities using the FindMultiModalNeighbors function, incorporating both PCA and LSI reductions. An additional UMAP was performed on the combined, weighted values were carried into cluster identification using the smart local moving (SLM) algorithm. Individual multi-modal samples were combined into a single, integrated object and harmonized for batch effects using the Harmony package. Position weight matrices (PWM) of transcription factor binding motifs were gathered from the JASPAR2020 database, which were then assembled using the CreateMotifMatrix function. The resulting matrix output was then used to generate a motif output that could be slotted into the prepared Seurat multi-modal object for genomic region-specific counts annotation. Chromatin Accessibility Variability Analysis (ChromVAR) was performed on each output to generate chromatin accessibility variability scores within labeled binding motifs following the hg38 genome reference.
Assembly: refdata-cellranger-arc-GRCh38-2020-A-2.0.0
Supplementary files format and content: MEX compatible cell-associated barcodes list
Supplementary files format and content: MEX compatible gene ID/name list
Supplementary files format and content: MEX format feature-barcode associated UMI count sparse matrix
Supplementary files format and content: BED-like tab file with captured ATAC fragments
Supplementary files format and content: HDF5 format feature-barcode UMI counts for scATAC-multiome
Supplementary files format and content: computed ATAX-GEX metrics per barcode
Library strategy: Multiome

molecule: other

extract_protocol:
Single Cell Sampling and Isolation  Biopsies for single cell processing were obtained from patients at the time of colonoscopy or upon undergoing abdominoperineal resection (completion proctectomy). At endoscopy, ~4 biopsies per region were collected by the physician for further single cell isolation. From proctectomy specimens, 10-20 biopsies per region were collected by the researcher using an endoscopic forceps prior to pathological grossing. To sample the fistula tract, a cross-section was first excised and then transected to expose the tract lining and facilitate biopsy acquisition. From surgical specimens with patent perianal fistulas, cross sections of the tract were resected with the assistance of the pathologist or pathology PA and preserved in O.C.T. Compound (Sakura) by the Mount Sinai Biorepository Core. FFPE specimens were retrieved from clinical samples previously processed and banked by the Biorepository.   Single Nucleus Isolation  Single cells from biopsies were isolated as described above. Nucleus isolation was carried out if the input cell count was within the range of 100,000 – 1,000,000. Cell lysis and all subsequent steps were carried out on ice or in a centrifuge at 4°C. All centrifugation steps post-lysis were for 5 min at 500 xg rcf. Cells were incubated in 100 L lysis buffer (0.1% NP-40 substitute [Sigma, 11754599001], 0.01% digitonin [MP Bio, 159480], 10% Tween-20 [Sigma, P7949] in wash buffer – 10 mM Tris-HCl pH 7.4 [Sigma, T2194], 10 mM NaCl, 3 mM MgCl2, 0.1% BSA, 1 mM DTT) for 3 min. Immediately upon the completion of lysis, 1 mL chilled wash buffer was added and the sample centrifuged. A total of 2-3 further washes were carried out; final nuclei counts were obtained during wash 2. The final centrifuged nucleus fraction was resuspended in a pre-determined volume of 1X Nucleus Buffer (10X Genomics, cat.no. 2000207) per the manufacturer’s guidelines and Nucleus Stock Concentration Table. A final nucleus count was performed to calculate the volume of nucleus stock in 1X buffer to carry forward into the initial Multiome transposition reaction. All nucleus preparation buffers contained 1U/L of RNase Inhibitor (Sigma, 3335399001).  After preparation of the nuclei, the 10X Genomics Single Cell ATAC + Gene Expression kit (PN-1000282) was carried out according to manufacturer’s instructions, and a targeted concentration of 10,000 nuclei were loaded per lane of the 10X Chromium Controller.
Nuclei were loaded on a Chromium Next GEM Chip J Single Cell Kit (PN-10002834) with GEMs from the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (PN-1000283) and indexed using the Dual Index Kit TT Set A (PN-1000215) and Single Index Kit N Set A (PN-1000212) according to 10x protocol CG000338 Rev D.


title: Perianal13_Rect_nuATAC


title: Perianal1_Transverse_cytoRNA

source_name: transverse colon biopsies

value: transverse colon biopsies


title: sample_208: Intestine from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: Intestine


title: sample_206: Intestine from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: sample_205: Intestine from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: Perianal12_Rect_nuATAC


title: sample_202: Kidney from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: sample_203: Kidney from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: Perianal12_Sig_nuRNA

molecule: nuclear RNA


title: Perianal13_Sig_nuRNA


title: sample_200: Kidney from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: sample_204: Kidney from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: Perianal13_Rect_nuRNA


title: Perianal12_Rect_nuRNA


title: sample_199: Kidney from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: sample_201: Kidney from PSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: Perianal10_Sig_nuATAC


title: Perianal10_Rect_nuATAC


title: sample_197: Liver from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge

value: 0 hrs

value: Liver


title: Perianal10_Sig_nuRNA


title: sample_196: Liver from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: Perianal10_Rect_nuRNA


title: sample_195: Liver from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: Perianal9_Sig_nuATAC


title: sample_194: Liver from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: Perianal9_Rect_nuATAC


title: Perianal9_Rect_nuRNA


title: sample_192: Intestine from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: Perianal9_Sig_nuRNA


title: sample_191: Intestine from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: Perianal12_Sig_nuATAC


title: Perianal5_Sig_nuATAC


title: sample_190: Intestine from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: Perianal5_Sig_nuRNA


title: Perianal5_Rect_nuRNA


title: sample_198: Liver from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: sample_188: Intestine from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: sample_187: Intestine from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: Perianal4_TI_nuATAC


title: Perianal5_Rect_nuATAC


title: sample_189: Intestine from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: Perianal4_TI_nuRNA


title: sample_183: Kidney from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: sample_185: Kidney from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: sample_178: Liver from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge

value: VSel

value: 48 hrs


title: sample_180: Liver from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_179: Liver from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_177: Liver from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_181: Kidney from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: sample_193: Liver from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: sample_176: Liver from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_175: Liver from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_174: Intestine from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_172: Intestine from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_170: Intestine from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_173: Intestine from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_169: Intestine from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_167: Kidney from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_168: Kidney from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_186: Kidney from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: sample_171: Intestine from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_165: Kidney from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_184: Kidney from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: sample_161: Liver from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: 24 hrs


title: sample_182: Kidney from PSel strain fish exposed to IHNV at timepoint 0 hrs post challenge


title: sample_166: Kidney from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_160: Liver from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_164: Kidney from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_163: Kidney from VSel strain fish exposed to IHNV at timepoint 48 hrs post challenge


title: sample_162: Liver from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_159: Liver from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_157: Liver from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_158: Liver from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_156: Intestine from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_155: Intestine from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_154: Intestine from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sample_153: Intestine from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: N87_shNC_1

city: Fuzhou

first: Sheng-Ze

middle: long

last: Wu

state: None Selected

address: NO.29,XINQUAN ROAD,FUZHOU 350001 FUJIAN PROVINCE,CHINA.

institute: Concord Hospital of the Fujian Medical University

data_processing:
Analyzing Sequence Quality with FastQC
Removing low quality sequences with Trim_Galore
Genome Comparison with STAR-aligner
Summarize gene counts with featureCounts
Generate an allegation analysis report using multiQC
Assembly: not provided
Supplementary files format and content: tab-delimiited text file includes raw counts, RPKM for each Sample

growth_protocol: NCI-N87 human gastric cancer cells were maintained in RMPI1640 supplemented with 10%FBS(Fetal Bovine Serum) and antibiotics in humidfied atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).1.3ug of tatol RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMATER Mrna-Seq Library Prep Kit following manufacturer's protocls

treatment_protocol: Cells were grown overnight to a density of 1×105 cells/well, then infected with viral supernatant at a multiplicity of infection of 10. To isolate stable clones, puromycin (2 μg/ml, Sigma) was utilized for a minimum duration of 1 week.

tag: cell line

value: human gastric cancer cells

value: shNC


title: N87_shNC_3

tag: cell type


title: N87_shONECUT2_3


title: N87_shONECUT2_2


title: sample_152: Intestine from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: N87_shONECUT2_1


title: EXO_NTN1_3

data_processing:
Illumina Casava2.19 software used for basecalling.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw counts for every miRNA and every sample

source_name: HUVEC derived exosomes

value: HUVEC derived exosomes


title: EXO_NTN1_2


title: EXO_Ctrl2

value: Ctrl


title: sample_151: Intestine from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: EXO_Ctrl3


title: EXO_NTN1_1


title: EXO_Ctrl1


title: sample_149: Kidney from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: Kidney


title: sciatic nerves, C3

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: Rnor_6.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: sciatic nerves

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: sciatic nerves

value: sciatic nerves 7 days post crush injury


title: sample_147: Kidney from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: IHNV


title: sciatic nerves, B2

description: 10x Genomics

value: sciatic nerves 3 days post crush injury


title: sample_148: Kidney from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sciatic nerves, C1

description: 10x Genomics


title: sciatic nerves, C2

description: 10x Genomics


title: sciatic nerves, A3

description: 10x Genomics

value: sham sciatic nerves


title: sciatic nerves, B3

description: 10x Genomics


title: sample_146: Kidney from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: N87_shNC_2


title: sciatic nerves, A2

description: 10x Genomics


title: sample_145: Kidney from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge


title: sciatic nerves, B1

description: 10x Genomics


title: sciatic nerves, A1

description: 10x Genomics


title: sample_144: Liver from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: 12 hrs


title: sample_143: Liver from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: sample_142: Liver from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: MO-9-CMP

city: Paris

first: Chloé

last: Arfeuille

address: 48, boulevard Sérurier

country: France

institute: APHP

data_processing:
Full Fastq files were aligned to the reference human genome hg19/GRCh37 with tophat2 (-p 24 -r 150 -g 2 --library-type fr-firststrand). Gene expression was quantified using the full Gencode v26lift37. We used HTSeq (Anders et al., 2015) to obtain the number of reads associated to each gene in the Gencode v26lift37 database (restricted to protein-coding genes, antisense and lincRNAs). Bioconductor DESeq package (Anders and Huber, 2010) was used to import raw HTSeq counts for each sample into R statistical software and extract the count matrix.
Assembly: hg19
Supplementary files format and content: FPKM file  in txt format

source_name: Bone Marrow

extract_protocol:
total RNA was extracted from mononuclear cells or sorted HSPC (1000 to 10000 cells) using the RNeasy Mini or Micro Kit (Qiagen).
Libraries were prepared with TruSeq® Stranded Total RNASample preparation kit (Illumina) according to supplier’s recommendations. Briefly the ribosomal RNA fraction was removed from 1μg of total RNA using the Ribo-Zero™ Gold Kit (Epicentre). Fragmentation was then achieved using divalent cations under elevated temperature to obtain approximately 300bp pieces. Double strand cDNA synthesis was performed using reverse transcriptase and random primers, Illumina adapters were ligated and cDNA library was PCR amplified for sequencing. Paired-end 75b sequencing was then carried out on a HiSeq4000 (Illumina).

treatment_protocol: CD34+ cells were selected from mononucleated cells using the Easysep Human CD34 positive selection kit and Easysep magnet (StemCell Technologies, Vancouver, Canada) following the manufacturer's instructions. Cells were phenotyped on a BD FACSCantoTM II analyzer (BD Biosciences) using marker combinations that have been validated in fetal and adult bone marrow (Notta et al., 2011, 2016):  CMP CD34+CD38+CD45RA-CD135+, GMP CD34+CD38+CD45RA+CD135+ and MEP CD34+CD38+CD45RA-CD135- .

value: Bone Marrow

value: Sorted  CMP

tag: sample type

value: Healthy postnatal

tag: jmml patients_unique_identifier

tag: age(wg

value: weeks of_gestation;y:years):6.8 Y

value: Yes


title: MO-9-GMP

value: Sorted  GMP

value: No


title: sample_150: Kidney from VSel strain fish exposed to IHNV at timepoint 24 hrs post challenge

value: VSel

value: 24 hrs


title: MO-9-MEP

value: Sorted  MEP


title: MO-6-MEP

value: weeks of_gestation;y:years):9.4 Y


title: MO-6-CMP


title: MO-05-MEP

value: weeks of_gestation;y:years):2.7 Y


title: sample_141: Liver from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: Liver


title: MO-6-GMP


title: MO-04-MEP

value: weeks of_gestation;y:years):2.2 Y


title: sample_139: Liver from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: IHNV


title: MO-05-GMP


title: MO-05-CMP


title: sample_138: Intestine from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: Intestine


title: MO-04-CMP


title: sample_140: Liver from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: 12 hrs


title: LMMJ-24-MEP

value: Bone Marrow

value: JMML

value: weeks of_gestation;y:years):4.4 Y


title: sample_137: Intestine from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: MO-04-GMP

value: Healthy postnatal


title: LMMJ-24-CMP

value: Sorted  CMP


title: sample_136: Intestine from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: LMMJ-23-MEP

value: weeks of_gestation;y:years):0.1 Y


title: LMMJ-23-GMP

value: Sorted  GMP

value: No


title: LMMJ-24-GMP


title: LMMJ-23-CMP


title: sample_135: Intestine from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: VSel


title: LMMJ-22-GMP

value: weeks of_gestation;y:years):0.6 Y


title: LMMJ-22-MEP

value: Sorted  MEP


title: sample_134: Intestine from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: LMMJ-22-CMP


title: LMMJ-20-GMP

value: weeks of_gestation;y:years):0.4 Y


title: LMMJ-20-CMP


title: sample_132: Kidney from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: Kidney


title: sample_133: Intestine from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: LMMJ-19-GMP

value: weeks of_gestation;y:years):3.4 Y


title: LMMJ-19-MEP


title: sample_131: Kidney from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: IHNV


title: LMMJ-19-CMP


title: sample_130: Kidney from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: LMMJ-17-GMP

value: weeks of_gestation;y:years):8.5 Y


title: LMMJ-17-CMP


title: LMMJ-15-GMP

value: weeks of_gestation;y:years):4.6 Y


title: sample_129: Kidney from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: 12 hrs


title: LMMJ-15-CMP

value: Bone Marrow

value: JMML


title: LMMJ-14-MEP

source_name: Peripheral blood

value: Peripheral blood

value: weeks of_gestation;y:years):0.2 Y


title: LMMJ-14-GMP


title: sample_128: Kidney from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge


title: LMMJ-14-CMP

value: Sorted  CMP


title: sample_126: Liver from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: 4 hrs

value: Liver


title: LMMJ-12-GMP

value: Sorted  GMP

value: weeks of_gestation;y:years):1.1 Y

value: No


title: sample_127: Kidney from VSel strain fish exposed to IHNV at timepoint 12 hrs post challenge

value: VSel


title: sample_125: Liver from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: LMMJ-12-MEP

value: Sorted  MEP


title: LMMJ-20-MEP

value: weeks of_gestation;y:years):0.4 Y


title: LMMJ-12-CMP


title: LMMJ-10-MEP

value: weeks of_gestation;y:years):2.4 Y


title: LMMJ-10-GMP


title: LMMJ-10-CMP

value: weeks of_gestation;y:years):4.1 Y

value: Yes


title: sample_124: Liver from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

value: IHNV


title: LMMJ-07-MEP

value: Bone Marrow


title: sample_123: Liver from VSel strain fish exposed to IHNV at timepoint 4 hrs post challenge


title: LMMJ-17-MEP

value: JMML

value: weeks of_gestation;y:years):8.5 Y


title: LMMJ-07-GMP


title: LMMJ-07-CMP


title: LMMJ-15-MEP

value: weeks of_gestation;y:years):4.6 Y